Correct breaking changes from new version

.github/workflows/CI.yml

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.6'
+          - '1.7'
           - '1.9'
           - 'nightly'
           - '1.10'

README.md

@@ -47,6 +47,7 @@ julia> out  = point_wise_minimization(P,T, data);
  Mode  :  0.24229  0.58808  0.14165  0.02798
 ```
 
+
 ### Example 2 - custom composition
 And here a case in which you specify your own bulk rock composition.
 ```julia
@@ -59,14 +60,14 @@ julia> sys_in  = "wt"
 julia> out     = single_point_minimization(P, T, data, X=X, Xoxides=Xoxides, sys_in=sys_in)
 Pressure          : 10.0      [kbar]
 Temperature       : 1100.0    [Celsius]
-     Stable phase | Fraction (mol 1 atom basis) 
-              liq   0.73698 
-              cpx   0.17241 
-             pl4T   0.04846 
-     Stable phase | Fraction (wt fraction) 
-              liq   0.70765 
-              cpx   0.18894 
-             pl4T   0.05083 
+     Stable phase | Fraction (mol fraction)
+              liq   0.73698
+              cpx   0.17241
+             pl4T   0.04846
+     Stable phase | Fraction (wt fraction)
+              liq   0.70765
+              cpx   0.18894
+             pl4T   0.05083
 Gibbs free energy : -907.392253  (22 iterations; 62.25 ms)
 Oxygen fugacity          : 3.400537515666476e-9
 ```
@@ -104,8 +105,6 @@ By default, this will show a progressbar (which you can deactivate with the `pro
 
 You can also specify a custom bulk rock for all points (see above), or a custom bulk rock for every point.
 
-
-
 ### Running it in parallel
 Julia can be run in parallel using multi-threading. To take advantage of this, you need to start julia from the terminal with:
 ```bash

julia/install_MAGEMin.jl

@@ -32,7 +32,7 @@ end
 
 write_environmental_variables_file()
 
-println("Succesfully downloaded the MAGEMin_jll package")
+println("Successfully downloaded the MAGEMin_jll package")
 println("And installed the environmental_variables.m file in: $(pwd())")
 
 # Show the version number

test/gen_tests_ig.jl

@@ -1,4 +1,4 @@
-# This script helps to generate a lsit of points for testing MAGEMin using reference built-in bulk-rock compositions
+# This script helps to generate a list of points for testing MAGEMin using reference built-in bulk-rock compositions
 
 cur_dir = pwd();    
 if  cur_dir[end-3:end]=="test"

test/gen_tests_mb.jl

@@ -1,4 +1,4 @@
-# This script helps to generate a lsit of points for testing MAGEMin using reference built-in bulk-rock compositions
+# This script helps to generate a list of points for testing MAGEMin using reference built-in bulk-rock compositions
 
 cur_dir = pwd();    
 if  cur_dir[end-3:end]=="test"

test/gen_tests_mp.jl

@@ -1,4 +1,4 @@
-# This script helps to generate a lsit of points for testing MAGEMin using reference built-in bulk-rock compositions
+# This script helps to generate a list of points for testing MAGEMin using reference built-in bulk-rock compositions
 
 cur_dir = pwd();    
 if  cur_dir[end-3:end]=="test"

test/tests.jl

@@ -46,7 +46,7 @@ finalize_MAGEMin(gv,DB,z_b)
     n       =   100;
     P       =   fill(8.0,n)
     T       =   fill(800.0,n)
-    db      =   "ig" 
+    db      =   "ig"
     data    =   Initialize_MAGEMin(db, verbose=false);
     out     =   multi_point_minimization(P, T, data, test=0);
     @test out[end].G_system ≈ -797.7491828675325
@@ -57,16 +57,16 @@ finalize_MAGEMin(gv,DB,z_b)
 end
 
 @testset "specify bulk rock" begin
-    
+
 
     data    = Initialize_MAGEMin("ig", verbose=false);
-    
+
     # One bulk rock for all points
     P,T     = 10.0, 1100.0
     Xoxides = ["SiO2"; "Al2O3"; "CaO"; "MgO"; "FeO"; "Fe2O3"; "K2O"; "Na2O"; "TiO2"; "Cr2O3"; "H2O"];
     X       = [48.43; 15.19; 11.57; 10.13; 6.65; 1.64; 0.59; 1.87; 0.68; 0.0; 3.0];
-    sys_in  = "wt"    
-    out     = single_point_minimization(P, T, data, X, Xoxides=Xoxides, sys_in=sys_in)
+    sys_in  = "wt"
+    out     = single_point_minimization(P, T, data, X=X, Xoxides=Xoxides, sys_in=sys_in)
 
     @test abs(out.G_system + 916.8283889543869)/abs(916.8283889543869) < 2e-4
 
@@ -78,9 +78,9 @@ end
     X1      = [48.43; 15.19; 11.57; 10.13; 6.65; 1.64; 0.59; 1.87; 0.68; 0.0; 3.0];
     X2      = [49.43; 14.19; 11.57; 10.13; 6.65; 1.64; 0.59; 1.87; 0.68; 0.0; 3.0];
     X       = [X1,X2]
-    sys_in  = "wt"    
-    out     = multi_point_minimization(P, T, data, X, Xoxides=Xoxides, sys_in=sys_in)
-    
+    sys_in  = "wt"
+    out     = multi_point_minimization(P, T, data, X=X, Xoxides=Xoxides, sys_in=sys_in)
+
     @test out[1].G_system ≈ -916.8283889543869 rtol=2e-4
     @test out[2].G_system ≈ -912.5920719174167 rtol=2e-4
 
@@ -100,13 +100,32 @@ end
     X = [[1.0], X]
     X_view = @view X[2,:]
 
-    out     = single_point_minimization(P, T, data, X_view, Xoxides=Xoxides, sys_in=sys_in)
+    out     = single_point_minimization(P, T, data, X=X_view, Xoxides=Xoxides, sys_in=sys_in)
 
     @test abs(out.G_system + 916.8283889543869)/abs(916.8283889543869) < 2e-4
 
     Finalize_MAGEMin(data)
 end
 
+@testset "view array PT" begin
+
+    data    = Initialize_MAGEMin("ig", verbose=false);
+
+    # different bulk rock per point
+    P       = [10.0, 10.0, 0]
+    T       = [1100.0, 1100.0, 0]
+    Xoxides = ["SiO2"; "Al2O3"; "CaO"; "MgO"; "FeO"; "Fe2O3"; "K2O"; "Na2O"; "TiO2"; "Cr2O3"; "H2O"];
+    X1      = [48.43; 15.19; 11.57; 10.13; 6.65; 1.64; 0.59; 1.87; 0.68; 0.0; 3.0];
+    X2      = [49.43; 14.19; 11.57; 10.13; 6.65; 1.64; 0.59; 1.87; 0.68; 0.0; 3.0];
+    X       = [X1,X2]
+    sys_in  = "wt"
+    P_view = @view P[1:2]
+    T_view = @view T[1:2]
+    out     = multi_point_minimization(P_view, T_view, data, X=X, Xoxides=Xoxides, sys_in=sys_in)
+
+    Finalize_MAGEMin(data)
+end
+
 @testset "convert bulk rock" begin
 
     bulk_in_ox = ["SiO2"; "Al2O3"; "CaO"; "MgO"; "FeO"; "Fe2O3"; "K2O"; "Na2O"; "TiO2"; "Cr2O3"; "H2O"];
@@ -148,9 +167,9 @@ end
 end
 
 # Stores data of tests
-mutable struct outP{ _T  } 
+mutable struct outP{ _T  }
     P           ::  _T
-    T           ::  _T 
+    T           ::  _T
     test        ::  Int64
 
     G           ::  _T
@@ -183,16 +202,16 @@ function VerifyPoint(out, list, i)
      # We need to sort the phases (sometimes they are ordered differently)
      ind_sol = sortperm(list.ph)
      ind_out = sortperm(out.ph)
-     
+
      result1 = @test out.G_system  ≈ list.G     rtol=1e-3
      result2 = @test out.ph[ind_out]        == list.ph[ind_sol]
      result3 = @test sort(out.ph_frac) ≈ sort(list.ph_frac) atol=5e-2       # ok, this is really large (needs fixing for test6!)
-     
+
      # print more info about the point if one of the tests above fails
      if isa(result1,Test.Fail) || isa(result2,Test.Fail) || isa(result3,Test.Fail)
          print_error_msg(i,list)
      end
-     
+
      return nothing
 end
 
@@ -204,7 +223,7 @@ println("Testing points from the reference diagrams:")
     println("  Starting KLB-1 peridotite tests")
     db  = "ig"  # database: ig, igneous (Holland et al., 2018); mp, metapelite (White et al 2014b)
     data = Initialize_MAGEMin(db, verbose=false);
-   
+
     gv.verbose=-1;
     @testset "IG-DB - KLB-1 peridotite" begin
         include("test_diagram_test0.jl")
@@ -220,7 +239,7 @@ println("Testing points from the reference diagrams:")
         include("test_diagram_test1.jl")
         TestPoints(list, data)
     end
-   
+
     println("  Starting Wet MORB tests")
     db          = "ig"  # database: ig, igneous (Holland et al., 2018); mp, metapelite (White et al 2014b)
     data = Initialize_MAGEMin(db, verbose=false);
@@ -234,7 +253,7 @@ println("Testing points from the reference diagrams:")
     println("  Starting WM Pelite tests")
     db  = "mp"  # database: ig, igneous (Holland et al., 2018); mp, metapelite (White et al 2014b)
     data = Initialize_MAGEMin(db, verbose=false);
-   
+
     gv.verbose=-1;
     @testset "MP-DB - WM Pelite" begin
         include("test_diagram_test0_mp.jl")
@@ -245,7 +264,7 @@ println("Testing points from the reference diagrams:")
     println("  Starting Gt-Migmatite tests")
     db  = "mp"  # database: ig, igneous (Holland et al., 2018); mp, metapelite (White et al 2014b)
     data = Initialize_MAGEMin(db, verbose=false);
-   
+
     gv.verbose=-1;
     @testset "MP-DB - Gt-Migmatite" begin
         include("test_diagram_test4_mp.jl")
@@ -257,13 +276,11 @@ println("Testing points from the reference diagrams:")
     println("  Starting SQA Amphibole tests")
     db  = "mb"  # database: ig, igneous (Holland et al., 2018); mp, metapelite (White et al 2014b)
     data = Initialize_MAGEMin(db, verbose=false, mbCpx = 1);
-   
+
     gv.verbose=-1;
     @testset "MB-DB - SQA Amphibole" begin
         include("test_diagram_test0_mb.jl")
         TestPoints(list, data)
     end
     Finalize_MAGEMin(data)
-
-
 end